Merge tag 'v1.0.20240202' into debian

* tag 'v1.0.20240202': (135 commits)
  Update submodules
  Refactor (rordenlab#791)
  gantry tilt tolerance (rordenlab#791)
  GE step description (rordenlab#790)
  PatientOrient -> Patient Position (rordenlab#786)
  Prevent shell expansion (rordenlab#789)
  Replace presumably accidental bitwise AND operations
  Update JasPer API calls for compatibility with newer versions of the library
  Update divest logic, reducing duplication and supporting new mode of operation
  Fix PhaseEncodingDirectionDisplayed for GE
  Update date
  GE Diffusion issue rordenlab#777 minor
  GE Diffusion issue rordenlab#777
  Kludge for issue 775 (rordenlab#775)
  add docstrings
  better python wrapper I/O
  issue 769: Mildly relax the check for bvec components > 1.
  PRs (rordenlab#745; rordenlab#768)
  Edge cases (rordenlab#763, rordenlab#749)
  Code spell
  ...

.appveyor.yml

@@ -0,0 +1,96 @@
+environment:
+  matrix:
+    - job_name: win
+      appveyor_build_worker_image: Visual Studio 2022
+
+    - job_name: linux
+      appveyor_build_worker_image: Ubuntu1604
+
+    - job_name: mac
+      appveyor_build_worker_image: macos-catalina
+
+matrix:
+  fast_finish: true
+
+version: build-{build}
+
+configuration: Release
+
+platform: x64
+
+clone_depth: 1
+
+init:
+  - ps: >-
+      $env:DATE = $(Get-Date -Format d-MMM-yyyy)
+
+      $githash = $env:APPVEYOR_REPO_COMMIT.Substring(0, 7)
+
+      $gittag = if ($env:APPVEYOR_REPO_TAG -eq $True) {"_$($env:APPVEYOR_REPO_TAG_NAME)"} else {""}
+
+      Update-AppveyorBuild -Version "$($env:DATE)_g${githash}${gittag}"
+
+      $env:RELEASE_VERSION = $(Get-Date -Format d-MMMM-yyyy)
+
+for:
+  -
+    matrix:
+      only:
+        - job_name: win
+
+    build_script:
+      - cmake -Wno-dev -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_OPENJPEG=GitHub -DUSE_JPEGLS=ON -B build
+      - cmake --build build --config %configuration%
+
+    after_build:
+      - 7z a dcm2niix_win.zip .\build\bin\* >$null
+      - appveyor PushArtifact dcm2niix_win.zip
+
+  -
+    matrix:
+      only:
+        - job_name: linux
+
+    build_script:
+      - export CC=gcc-8 CXX=g++-8
+      - cmake -Wno-dev -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_OPENJPEG=GitHub -DUSE_JPEGLS=ON -B build
+      - cmake --build build
+
+    after_build:
+      - strip -sx build/bin/*
+      - 7z a dcm2niix_lnx.zip ./build/bin/* &>/dev/null
+      - appveyor PushArtifact dcm2niix_lnx.zip
+
+  -
+    matrix:
+      only:
+        - job_name: mac
+
+    build_script:
+      - sudo xcode-select -s /Applications/Xcode-11.3.1.app
+      - cmake -Wno-dev -DCMAKE_OSX_ARCHITECTURES=x86_64 -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_OPENJPEG=GitHub -DUSE_JPEGLS=ON -B intel
+      - cmake --build intel
+      - sudo xcode-select -s /Applications/Xcode-12.3.app
+      - cmake -Wno-dev -DCMAKE_OSX_ARCHITECTURES=arm64 -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_OPENJPEG=GitHub -DUSE_JPEGLS=ON -B apple
+      - cmake --build apple
+
+    after_build:
+      - mkdir -p build/bin
+      - lipo -create -output build/bin/dcm2niix intel/bin/dcm2niix apple/bin/dcm2niix
+      - strip -Sx build/bin/*
+      - 7z a dcm2niix_mac.zip ./build/bin/* &>/dev/null
+      - appveyor PushArtifact dcm2niix_mac.zip
+
+deploy:
+  - provider: GitHub
+    tag: $(APPVEYOR_REPO_TAG_NAME)
+    release: version $(RELEASE_VERSION) ($(APPVEYOR_REPO_TAG_NAME))
+    description: ""
+    auth_token:
+      secure: gCltVLQEWsjSTRlsi8qw7FGP54ujBq60apjXkWTV954b65bOHl95hXMxxkQ734L4
+    artifact: /dcm2niix_.*\.zip/
+    draft: false
+    prerelease: false
+    on:
+      branch: master
+      APPVEYOR_REPO_TAG: true

.codespellrc

@@ -0,0 +1,11 @@
+[codespell]
+skip = .git,*.json,dcm_qa*
+# te - the TE used in the code often
+# clen - another common variable for length of smth
+# tage - for \tAge, inline ignores are yet to be released
+# nd - there is some kind of ND whi
+# ❯ grep -e 'trace or MD ' -e 'Trace/ND' ./console/nii_dicom_batch.cpp
+#		// the isotropic trace or MD can be calculated) often come as
+#			/*if (!dcmList[indx0].isDerived) //no need to warn if images are derived Trace/ND pair
+# ser - used in  printMessage(" acq %d img %d ser %ld ...
+ignore-words-list = te,clen,tage,nd,ser

.github/ISSUE_TEMPLATE/bug_report.md

@@ -42,6 +42,6 @@ Please try the following steps to resolve your issue:
 ```
 git clone --branch development https://github.com/rordenlab/dcm2niix.git
 cd dcm2niix/console
-g++  -I.  main_console.cpp nii_foreign.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp  -o dcm2niix -DmyDisableOpenJPEG
+make
 ./dcm2niix ....
 ```

.github/workflows/codespell.yml

@@ -0,0 +1,19 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [development,master]
+  pull_request:
+    branches: [development,master]
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v1

.gitignore

@@ -2,3 +2,14 @@
 /build/
 /bin/
 /console/dcm2niix
+# Python wrapper
+*.py[co]
+*.so
+__pycache__/
+/_skbuild/
+/_cmake_test_compile/
+/dcm2niix/_dist_ver.py
+/dcm2niix/dcm2niix
+MANIFEST
+/*.egg*/
+/dist/